[BioC] problems reading Illumina files using BeadExplorer
Vitalina Komashko
vmkomashko at ucdavis.edu
Thu Oct 26 02:30:20 CEST 2006
Dear all,
I am trying to use BeadExplorer to load Illumina Mouse8 arrays for
analysis.
I used the latest BeadStudio software version to generate expression
data, but it actually does not give summary files such as
gene.profile.csv and qcinfo.csv, so I had to save them separately when I
opened the data. Here the error I constantly get when I load the data:
> data<-beadAnalysis()
Read C:/Program Files/R/R-2.4.0/data/mouse_copy_sample_gene_profile.csv
Normalised data...
Generated qc data...
Error in sum(detExprs(beadData)[, i] > value) :
subscript out of bounds
In addition: Warning message:
no non-missing arguments to min; returning Inf
There are no header lines when I save my data directly from BeadStudio.
Does it matter?
R info:
> sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] "tools" "tcltk" "methods" "stats" "graphics" "grDevices"
[7] "utils" "datasets" "base"
other attached packages:
convert marray limma BeadExplorer tkWidgets
DynDoc
"1.8.0" "1.12.0" "2.9.1" "1.2.0" "1.12.0"
"1.12.0"
R2HTML affy affyio widgetTools Biobase
"1.58" "1.12.0" "1.2.0" "1.10.0" "1.12.1"
I will appreciate any help. Thank you!
Vitalina.
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